Sun Oct 9 16:15:06 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 16:15:06 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3147 !!! WARNING: GLM 233 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6020021 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -15.68300 37.54800 ymin,ymax (A): 3.265000 55.91900 zmin,zma (A): -34.57100 24.56500 x,y,z range (A): 53.23100 52.65400 59.13600 scale (grids/A): 0.6020021 object centre (A): 10.93250 29.59200 -5.002999 number of atom coordinates read : 3147 total number of charged atoms : 2999 net assigned charge : -5.593977 assigned positive charge : 467.2409 centred at (gu) : 89.97027 91.10064 88.21794 assigned negative charge : -472.8364 centred at (gu) : 90.01917 91.21245 88.15791 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7418 nv = 96 ne = 84 npr = 65266 no. pairs analyzed = 65266 no. exposed pairs = 3751 no. arc points = 26194 no. surface atoms = 1278 nbur = 1869 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 394 mr = 4097 m= 2 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 33 time to turn everything in is 0.3200000 number of dielectric boundary points 3672 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2645 ## 265 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 9427 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.8934956E-09 2.2075190E-10 midg,1,midg; midg,igrid,midg 2.1293292E-09 -9.9616022E-09 1,midg,midg; igrid,midg,midg -1.3322238E-10 -4.7017608E-09 gauss-seidel spectral radius is 0.9857611 estimated iterations to convergence 69 setup time was (sec) 0.5400000 now iterating at: 16:15:07 rms-change max change #iterations 0.1265998 17.96655 at 10iterations 1.0854192E-02 1.658897 at 20iterations 9.6249598E-04 0.1666260 at 30iterations 1.1090113E-04 1.8226624E-02 at 40iterations 2.6209351E-05 5.3405762E-03 at 50iterations finished qdiffx linear iterations at : 16:15:09 total time elapsed so far: 2.940000 # loops : 50 mean,max change (kT/e) : 2.6209351E-05 5.3405762E-03 energy calculations done at 2.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.120000 DelPhi exited at 16:15:10 3.122u 0.131s 0:03.52 92.3% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 16:15:10 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3147 !!! WARNING: GLM 233 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.806006 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -15.68300 37.54800 ymin,ymax (A): 3.265000 55.91900 zmin,zma (A): -34.57100 24.56500 x,y,z range (A): 53.23100 52.65400 59.13600 scale (grids/A): 1.806006 object centre (A): 10.93250 29.59200 -5.002999 number of atom coordinates read : 3147 total number of charged atoms : 2999 net assigned charge : -5.593977 assigned positive charge : 467.2409 centred at (gu) : 89.90965 93.30097 84.65301 assigned negative charge : -472.8364 centred at (gu) : 90.05737 93.63692 84.47313 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 81832 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26194 grid for indexing accessible points = 1.400000 m= 28053 mr = 57375 m= 4195 mr = 20396 m= 218 mr = 2514 m= 2 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 602 time to turn everything in is 0.5600000 number of dielectric boundary points 33954 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 176 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 23443 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.6020021 object centre at (A) : 10.93250 29.59200 -5.002999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.7182101E-03 2.3807462E-03 midg,1,midg; midg,igrid,midg -1.3241330E-02 -2.3659276E-02 1,midg,midg; igrid,midg,midg -2.2738701E-02 -1.9233750E-02 gauss-seidel spectral radius is 0.9985304 estimated iterations to convergence 207 setup time was (sec) 0.8300000 now iterating at: 16:15:11 rms-change max change #iterations 4.294052 170.7725 at 10iterations 1.944819 64.59553 at 20iterations 0.8836856 29.98219 at 30iterations 0.4027381 12.32687 at 40iterations 0.1830236 5.796980 at 50iterations 8.3381817E-02 2.635651 at 60iterations 3.8004525E-02 1.243116 at 70iterations 1.7315393E-02 0.5735397 at 80iterations 7.8896936E-03 0.2205200 at 90iterations 3.5895426E-03 0.1209927 at 100iterations 1.6464879E-03 4.7164917E-02 at 110iterations 7.5066433E-04 2.1584272E-02 at 120iterations finished qdiffx linear iterations at : 16:15:17 total time elapsed so far: 6.880000 # loops : 120 mean,max change (kT/e) : 7.5066433E-04 2.1584272E-02 energy calculations done at 6.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.060000 DelPhi exited at 16:15:17 7.060u 0.152s 0:07.53 95.7% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 16:15:17 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3147 !!! WARNING: GLM 233 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.709010 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -15.68300 37.54800 ymin,ymax (A): 3.265000 55.91900 zmin,zma (A): -34.57100 24.56500 x,y,z range (A): 53.23100 52.65400 59.13600 scale (grids/A): 2.709010 object centre (A): 10.93250 29.59200 -5.002999 number of atom coordinates read : 3147 total number of charged atoms : 2999 net assigned charge : -5.593977 assigned positive charge : 467.2409 centred at (gu) : 89.86427 94.95123 81.97925 assigned negative charge : -472.8364 centred at (gu) : 90.08598 95.45536 81.70969 start vw surface at 0.1900000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 190311 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26194 grid for indexing accessible points = 1.400000 m= 92495 mr = 140265 m= 32107 mr = 74969 m= 7345 mr = 25323 m= 913 mr = 5368 m= 39 mr = 552 m= 0 mr = 19 time to grow re-entrant surface = 0.8100000 no. cavity mid-points inaccessible to solvent = 2129 time to turn everything in is 1.420000 number of dielectric boundary points 76714 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.550000 number of grid points assigned charge 23992 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.806006 object centre at (A) : 10.93250 29.59200 -5.002999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.4296565E-02 0.1261248 midg,1,midg; midg,igrid,midg -0.2222733 -0.2561494 1,midg,midg; igrid,midg,midg -0.3510340 -0.2515876 gauss-seidel spectral radius is 0.9992388 estimated iterations to convergence 286 setup time was (sec) 1.700000 now iterating at: 16:15:19 rms-change max change #iterations 10.27013 317.3109 at 10iterations 5.978956 137.8162 at 20iterations 3.460283 71.50179 at 30iterations 1.988097 41.45322 at 40iterations 1.143615 23.21748 at 50iterations 0.6549792 16.65956 at 60iterations 0.3750815 7.068957 at 70iterations 0.2153878 3.806253 at 80iterations 0.1228659 2.531574 at 90iterations 7.0357725E-02 1.316910 at 100iterations 4.0256143E-02 0.8078671 at 110iterations 2.2958145E-02 0.4555616 at 120iterations 1.3118352E-02 0.2627678 at 130iterations 7.4857706E-03 0.1372223 at 140iterations 4.2680940E-03 8.1804276E-02 at 150iterations 2.4369694E-03 4.1889191E-02 at 160iterations 1.3901971E-03 2.4230957E-02 at 170iterations 7.9429976E-04 1.3280869E-02 at 180iterations finished qdiffx linear iterations at : 16:15:29 total time elapsed so far: 11.11000 # loops : 180 mean,max change (kT/e) : 7.9429976E-04 1.3280869E-02 energy calculations done at 11.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.29000 DelPhi exited at 16:15:29 11.290u 0.174s 0:11.73 97.6% 0+0k 0+0io 0pf+0w